CA2500603A1 - Gene expression profiling from ffpe samples - Google Patents

Gene expression profiling from ffpe samples Download PDF

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Publication number
CA2500603A1
CA2500603A1 CA002500603A CA2500603A CA2500603A1 CA 2500603 A1 CA2500603 A1 CA 2500603A1 CA 002500603 A CA002500603 A CA 002500603A CA 2500603 A CA2500603 A CA 2500603A CA 2500603 A1 CA2500603 A1 CA 2500603A1
Authority
CA
Canada
Prior art keywords
data
rna
expression
sample
gene expression
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Abandoned
Application number
CA002500603A
Other languages
English (en)
French (fr)
Inventor
Mark G. Erlander
Ranelle Salunga
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Life Technologies Corp
Original Assignee
Individual
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Individual filed Critical Individual
Publication of CA2500603A1 publication Critical patent/CA2500603A1/en
Abandoned legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
CA002500603A 2002-10-11 2003-10-10 Gene expression profiling from ffpe samples Abandoned CA2500603A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US41810302P 2002-10-11 2002-10-11
US60/418,103 2002-10-11
US10/329,282 2002-12-23
US10/329,282 US7364846B2 (en) 2002-10-11 2002-12-23 Gene expression profiling from FFPE samples
PCT/US2003/032345 WO2004033660A2 (en) 2002-10-11 2003-10-10 Gene expression profiling from ffpe samples

Publications (1)

Publication Number Publication Date
CA2500603A1 true CA2500603A1 (en) 2004-04-22

Family

ID=32072932

Family Applications (1)

Application Number Title Priority Date Filing Date
CA002500603A Abandoned CA2500603A1 (en) 2002-10-11 2003-10-10 Gene expression profiling from ffpe samples

Country Status (9)

Country Link
US (10) US7364846B2 (de)
EP (3) EP1549769B1 (de)
JP (1) JP2006501857A (de)
AT (1) ATE527377T1 (de)
AU (1) AU2003282608A1 (de)
CA (1) CA2500603A1 (de)
MX (1) MXPA05003818A (de)
NZ (1) NZ539124A (de)
WO (1) WO2004033660A2 (de)

Families Citing this family (15)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7364846B2 (en) * 2002-10-11 2008-04-29 Molecular Devices Corporation Gene expression profiling from FFPE samples
MY138544A (en) * 2003-06-26 2009-06-30 Neuramatix Sdn Bhd Neural networks with learning and expression capability
EP1654361B2 (de) † 2003-07-25 2023-01-18 Life Technologies Corporation Verfahren und zusammensetzungen zur herstellung von rna aus einer fixierten probe
WO2006132971A2 (en) 2005-06-03 2006-12-14 Aviaradx, Inc. Identification of tumors and tissues
US7451122B2 (en) * 2006-03-29 2008-11-11 Honeywell International Inc. Empirical design of experiments using neural network models
JP2008043332A (ja) * 2006-08-17 2008-02-28 Panomics Inc 組織スライドからの核酸定量
US20120196768A1 (en) * 2010-04-22 2012-08-02 Toray Industries, Inc. METHOD FOR PREPARING aRNA AND METHOD FOR ANALYSIS OF GENE EXPRESSION
TWI425977B (zh) 2010-11-24 2014-02-11 Ind Tech Res Inst 將福馬林固定石蠟包埋之組織進行脫蠟的方法與其套組
EP2468862A1 (de) * 2010-12-23 2012-06-27 Qiagen GmbH Verfahren und Kit zur Verarbeitung von in Wachs eingebetteten biologischen Proben
WO2013010074A1 (en) 2011-07-13 2013-01-17 Primeradx, Inc. Multimodal methods for simultaneous detection and quantification of multiple nucleic acids in a sample
JP2014533952A (ja) 2011-11-17 2014-12-18 リーアニクス・インコーポレイテッドＲｈｅｏｎｉｘ， Ｉｎｃ． 微小流体装置、方法および応用
CA2897360C (en) * 2013-01-24 2017-01-03 F. Hoffmann-La Roche Ag Rt-qpcr analysis of micro-dissected material from stained ffpet section
WO2014160645A2 (en) 2013-03-15 2014-10-02 Biotheranostics, Inc. Neuroendocrine tumors
US20170045421A1 (en) 2015-08-10 2017-02-16 Life Technologies Corporation Devices and methods for laser capture microdissection
CN111528219B (zh) * 2020-05-13 2022-03-15 上海市计量测试技术研究院 一种用于t淋巴细胞亚群计数标准物质的冻干保护剂及其应用

Family Cites Families (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4675297A (en) * 1981-02-23 1987-06-23 The Regents Of The University Of California Genes encoding bovine prolactin
US5545522A (en) 1989-09-22 1996-08-13 Van Gelder; Russell N. Process for amplifying a target polynucleotide sequence using a single primer-promoter complex
US5155018A (en) * 1991-07-10 1992-10-13 Hahnemann University Process and kit for isolating and purifying RNA from biological sources
DE4321904B4 (de) * 1993-07-01 2013-05-16 Qiagen Gmbh Verfahren zur chromatographischen Reinigung und Trennung von Nucleinsäuregemischen
CA2153215A1 (en) 1994-07-06 1996-01-07 Lu Wang Treatment of paraffin embedded tissue for gene analysis
US5698410A (en) * 1995-06-07 1997-12-16 Mount Sinai School Of Medicine Of The City University Of New York Highly sensitive immunocytochemical method for diagnosis of malignant effusions
US5981235A (en) * 1996-07-29 1999-11-09 Promega Corporation Methods for isolating nucleic acids using alkaline protease
AU6854098A (en) * 1997-04-18 1998-11-13 Chugai Research Institute For Molecular Medicine, Inc. Transcriptional regulator
US6183995B1 (en) 1997-09-05 2001-02-06 Lifespan Biosciences, Inc. Methods of measuring gene expression using wax-embedded tissue specimens
US5932451A (en) * 1997-11-19 1999-08-03 Incyte Pharmaceuticals, Inc. Method for unbiased mRNA amplification
ATE260989T1 (de) * 1997-12-19 2004-03-15 Affymetrix Inc Erkenntnisse der genomforschung für die suche nach neuartigen wirkstoffen
US6136537A (en) * 1998-02-23 2000-10-24 Macevicz; Stephen C. Gene expression analysis
US6218122B1 (en) 1998-06-19 2001-04-17 Rosetta Inpharmatics, Inc. Methods of monitoring disease states and therapies using gene expression profiles
DE19856064C2 (de) * 1998-12-04 2000-11-30 Invitek Gmbh Universelles Verfahren zur Isolierung von DNA aus beliebigen Ausgangsmaterialien
US6429027B1 (en) * 1998-12-28 2002-08-06 Illumina, Inc. Composite arrays utilizing microspheres
US6248535B1 (en) 1999-12-20 2001-06-19 University Of Southern California Method for isolation of RNA from formalin-fixed paraffin-embedded tissue specimens
US20020081597A1 (en) * 2000-03-31 2002-06-27 Genentech, Inc. Compositions and methods for detecting and quantifying gene expression
AU2001272908A1 (en) * 2000-05-10 2001-11-20 David A. Sirbasku Compositions and methods for the diagnosis, treatment and prevention of steroid hormone responsive cancers
US7666586B2 (en) * 2000-06-30 2010-02-23 Aros Applied Biotechnology Aps Gene expression in biological conditions
US6713257B2 (en) * 2000-08-25 2004-03-30 Rosetta Inpharmatics Llc Gene discovery using microarrays
US6794141B2 (en) 2000-12-22 2004-09-21 Arcturus Bioscience, Inc. Nucleic acid amplification
JP2002262882A (ja) * 2001-03-12 2002-09-17 Nisshinbo Ind Inc Ｒｎａの増幅法
WO2002074979A2 (en) 2001-03-20 2002-09-26 Ortho-Clinical Diagnostics, Inc. Expression profiles and methods of use
US7214373B2 (en) * 2001-07-24 2007-05-08 Yale University Methods, compositions and kits relating to chitinases and chitinase-like molecules and inflammatory disease
US9201067B2 (en) 2003-03-05 2015-12-01 Posco Size-controlled macromolecule
DK2258872T3 (da) 2002-03-13 2013-11-18 Genomic Health Inc Genekspressionsprofilering i biopsier af tumorvæv
US7364846B2 (en) * 2002-10-11 2008-04-29 Molecular Devices Corporation Gene expression profiling from FFPE samples

Also Published As

Publication number Publication date
US20100197511A1 (en) 2010-08-05
US20090082215A1 (en) 2009-03-26
US7723039B2 (en) 2010-05-25
US8895269B2 (en) 2014-11-25
EP2330217A1 (de) 2011-06-08
US20180094297A1 (en) 2018-04-05
EP1549769A2 (de) 2005-07-06
US20200362393A1 (en) 2020-11-19
WO2004033660A2 (en) 2004-04-22
EP2484777A1 (de) 2012-08-08
WO2004033660A3 (en) 2004-08-26
NZ539124A (en) 2008-12-24
US7364846B2 (en) 2008-04-29
US20120316084A1 (en) 2012-12-13
US20150152478A1 (en) 2015-06-04
MXPA05003818A (es) 2005-10-05
US20040072305A1 (en) 2004-04-15
EP1549769A4 (de) 2007-04-25
US8012688B2 (en) 2011-09-06
US8435739B2 (en) 2013-05-07
US20120245046A1 (en) 2012-09-27
AU2003282608A1 (en) 2004-05-04
US20110034346A1 (en) 2011-02-10
US7879555B2 (en) 2011-02-01
US20150225776A1 (en) 2015-08-13
EP1549769B1 (de) 2011-10-05
JP2006501857A (ja) 2006-01-19
ATE527377T1 (de) 2011-10-15

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EEER Examination request
FZDE Discontinued